Variant report

Variant	rs9980087
Chromosome Location	chr21:46112455-46112456
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11909180	0.98[ASN][1000 genomes]
rs12481809	0.81[ASN][1000 genomes]
rs12483730	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2243667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2838615	0.85[CHD][hapmap]
rs2838616	0.85[CHD][hapmap]
rs2838626	0.85[GIH][hapmap]
rs2838630	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2838639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2838645	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[ASN][1000 genomes]
rs2838649	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2838654	1.00[JPT][hapmap]
rs28797484	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818956	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4818962	0.80[ASN][1000 genomes]
rs55914221	0.81[ASN][1000 genomes]
rs56829302	0.92[ASN][1000 genomes]
rs60154040	0.95[ASN][1000 genomes]
rs60327918	0.98[ASN][1000 genomes]
rs60681728	0.98[ASN][1000 genomes]
rs7283084	0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7283406	0.86[CHB][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs8132905	0.95[ASN][1000 genomes]
rs8133996	1.00[JPT][hapmap]
rs9637188	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9974365	0.81[ASN][1000 genomes]
rs9975249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9978932	1.00[JPT][hapmap]
rs9981523	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981573	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9981618	0.98[ASN][1000 genomes]
rs9982002	0.98[ASN][1000 genomes]
rs9984476	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9980087	PWP2	cis	parietal	SCAN
rs9980087	KRTAP12-3	cis	cerebellum	SCAN
rs9980087	KRTAP10-3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46101000-46122200	Weak transcription	Right Atrium	heart
2	chr21:46107600-46114800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr21:46107800-46114200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr21:46109000-46114800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:46111400-46112600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr21:46112000-46114800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr21:46112000-46114800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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